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1. scGHSOM: Hierarchical clustering and visualization of single-cell and CRISPR data using growing hierarchical SOM

Author

Wen, Shang-Jung, Chang, Jia-Ming, and Yu, Fang

Subjects
Computer Science - Machine Learning, Computer Science - Information Retrieval, Quantitative Biology - Genomics
Abstract

High-dimensional single-cell data poses significant challenges in identifying underlying biological patterns due to the complexity and heterogeneity of cellular states. We propose a comprehensive gene-cell dependency visualization via unsupervised clustering, Growing Hierarchical Self-Organizing Map (GHSOM), specifically designed for analyzing high-dimensional single-cell data like single-cell sequencing and CRISPR screens. GHSOM is applied to cluster samples in a hierarchical structure such that the self-growth structure of clusters satisfies the required variations between and within. We propose a novel Significant Attributes Identification Algorithm to identify features that distinguish clusters. This algorithm pinpoints attributes with minimal variation within a cluster but substantial variation between clusters. These key attributes can then be used for targeted data retrieval and downstream analysis. Furthermore, we present two innovative visualization tools: Cluster Feature Map and Cluster Distribution Map. The Cluster Feature Map highlights the distribution of specific features across the hierarchical structure of GHSOM clusters. This allows for rapid visual assessment of cluster uniqueness based on chosen features. The Cluster Distribution Map depicts leaf clusters as circles on the GHSOM grid, with circle size reflecting cluster data size and color customizable to visualize features like cell type or other attributes. We apply our analysis to three single-cell datasets and one CRISPR dataset (cell-gene database) and evaluate clustering methods with internal and external CH and ARI scores. GHSOM performs well, being the best performer in internal evaluation (CH=4.2). In external evaluation, GHSOM has the third-best performance of all methods., Comment: Abstract presentation at BIOKDD@ACM KDD 2024

Published
2024

5. Case Classification System Based on Taiwanese Civil Summary Court Cases

Author

Chen, Ming-Yi, Chang, Jia-Wei, Lo, Hsiao-Chin, Pu, Ying-Hung, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Zhang, Junjie James, Series Editor, Tan, Kay Chen, Series Editor, Hung, Jason C., editor, Yen, Neil, editor, and Chang, Jia-Wei, editor

Published
2024
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6. Design of a Fair Distributed Computing Platform Based on Distributed Ledger Technology and Performance Measurements

Author

Liao, Bo-Yan, Chang, Jia-Wei, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Zhang, Junjie James, Series Editor, Tan, Kay Chen, Series Editor, Hung, Jason C., editor, Yen, Neil, editor, and Chang, Jia-Wei, editor

Published
2024
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7. Exploring the Potential of Webcam-Based Eye-Tracking for Traditional Eye-Tracking Analysis

Author

Chang, Cheng-Hui, Hung, Jason C., Chang, Jia-Wei, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Zhang, Junjie James, Series Editor, Tan, Kay Chen, Series Editor, Hung, Jason C., editor, Yen, Neil, editor, and Chang, Jia-Wei, editor

Published
2024
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8. A Survey of Speech Recognition for People with Cerebral Palsy

Author

Wu, Yu-Ru, Hung, Jason C., Chang, Jia-Wei, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Zhang, Junjie James, Series Editor, Tan, Kay Chen, Series Editor, Hung, Jason C., editor, Yen, Neil, editor, and Chang, Jia-Wei, editor

Published
2024
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10. Fuzzy Proximity Two-Dimension Inductance Gesture Recognition System Analysis and Implement

Author

Chu, Chao-Ting, Chang, Jia-Wei, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Hirche, Sandra, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Tan, Kay Chen, Series Editor, Pei, Yan, editor, Ma, Hao Shang, editor, Chan, Yu-Wei, editor, and Jeong, Hwa-Young, editor

Published
2024
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11. Proximity Capacitive Gesture Recognition for Recursive Neighbor Memory Neural Network

Author

Chu, Chao-Ting, Chang, Jia-Wei, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Hirche, Sandra, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Tan, Kay Chen, Series Editor, Pei, Yan, editor, Ma, Hao Shang, editor, Chan, Yu-Wei, editor, and Jeong, Hwa-Young, editor

Published
2024
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12. Design on Experimental Dataset and Task for Teaching in Data Science and Machine Learning

Author

Chen, Zhen, Guo, Min, Deng, Li-Rui, Zheng, Wen-Xun, Wang, Hao, Chang, Jia-hui, Zhang, Yi-song, Ma, Xiao-Dong, Gao, Ying, Wang, Hao-Yu, Lu, Xin, Li, Chao, Zhou, Jin, Li, Shuang Shou, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Hong, Wenxing, editor, and Kanaparan, Geetha, editor

Published
2024
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13. Atlas-Based Path Synthesis of Planar Four-Bar Linkages Using Elliptical Fourier Descriptors

Author

Chang, Yuan, Chang, Jia-Ling, Lee, Jyh-Jone, Ceccarelli, Marco, Series Editor, Agrawal, Sunil K., Advisory Editor, Corves, Burkhard, Advisory Editor, Glazunov, Victor, Advisory Editor, Hernández, Alfonso, Advisory Editor, Huang, Tian, Advisory Editor, Jauregui Correa, Juan Carlos, Advisory Editor, Takeda, Yukio, Advisory Editor, and Okada, Masafumi, editor

Published
2024
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15. P. gingivalis in oral-prostate axis exacerbates benign prostatic hyperplasia via IL-6/IL-6R pathway

Author

Shuang-Ying Wang, Yi Cai, Xiao Hu, Fei Li, Xin-Hang Qian, Ling-Yun Xia, Bo Gao, Lan Wu, Wen-Zhong Xie, Jia-Min Gu, Tong Deng, Cong Zhu, Hai-Chang Jia, Wan-Qi Peng, Jiao Huang, Cheng Fang, and Xian-Tao Zeng

Subjects
Porphyromonas gingivalis, Benign prostatic hyperplasia, Periodontitis, Oral pathogens, Inflammation, Medicine (General), R5-920, Military Science
Abstract

Abstract Background Benign prostatic hyperplasia (BPH) is the most common disease in elderly men. There is increasing evidence that periodontitis increases the risk of BPH, but the specific mechanism remains unclear. This study aimed to explore the role and mechanism of the key periodontal pathogen Porphyromonas gingivalis (P. gingivalis) in the development of BPH. Methods The subgingival plaque (Sp) and prostatic fluid (Pf) of patients with BPH concurrent periodontitis were extracted and cultured for 16S rDNA sequencing. Ligature-induced periodontitis, testosterone-induced BPH and the composite models in rats were established. The P. gingivalis and its toxic factor P. gingivalis lipopolysaccharide (P.g-LPS) were injected into the ventral lobe of prostate in rats to simulate its colonization of prostate. P.g-LPS was used to construct the prostate cell infection model for mechanism exploration. Results P. gingivalis, Streptococcus oralis, Capnocytophaga ochracea and other oral pathogens were simultaneously detected in the Pf and Sp of patients with BPH concurrent periodontitis, and the average relative abundance of P. gingivalis was found to be the highest. P. gingivalis was detected in both Pf and Sp in 62.5% of patients. Simultaneous periodontitis and BPH synergistically aggravated prostate histological changes. P. gingivalis and P.g-LPS infection could induce obvious hyperplasia of the prostate epithelium and stroma (epithelial thickness was 2.97- and 3.08-fold that of control group, respectively), and increase of collagen fibrosis (3.81- and 5.02-fold that of control group, respectively). P. gingivalis infection promoted prostate cell proliferation, inhibited apoptosis, and upregulated the expression of inflammatory cytokines interleukin-6 (IL-6; 4.47-fold), interleukin-6 receptor-α (IL-6Rα; 5.74-fold) and glycoprotein 130 (gp130; 4.47-fold) in prostatic tissue. P.g-LPS could significantly inhibit cell apoptosis, promote mitosis and proliferation of cells. P.g-LPS activates the Akt pathway through IL-6/IL-6Rα/gp130 complex, which destroys the imbalance between proliferation and apoptosis of prostate cells, induces BPH. Conclusion P. gingivalis was abundant in the Pf of patients with BPH concurrent periodontitis. P. gingivalis infection can promote BPH, which may affect the progression of BPH via inflammation and the Akt signaling pathway.

Published
2024
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16. Changes in disease burden and global inequalities in bladder, kidney and prostate cancers from 1990 to 2019: a comparative analysis based on the global burden of disease study 2019

Author

Qiao Huang, Jun Yang, Guo-Xiong Liu, Hao Zi, Shi-Di Tang, Hai-Chang Jia, Wei Li, Xiao-Feng Xu, and Xian-Tao Zeng

Subjects
Burden of disease, Bladder cancer, Kidney cancer, Prostate cancer, Health inequality, Public aspects of medicine, RA1-1270
Abstract

Abstract Background Bladder, kidney and prostate cancers make significant contributors to cancer burdens. Exploring their cross-country inequalities may inform equitable strategies to meet the 17 sustainable development goals before 2030. Methods We analyzed age-standardized disability-adjusted life-years (ASDALY) rates for the three cancers based on Global Burden of Diseases Study 2019. We quantified the inequalities using slope index of inequality (SII, absolute measure) and concentration index (relative measure) associated with national sociodemographic index. Results Varied ASDALY rates were observed in the three cancers across 204 regions. The SII decreased from 35.15 (95% confidence interval, CI: 29.34 to 39.17) in 1990 to 15.81 (95% CI: 7.99 to 21.79) in 2019 for bladder cancers, from 78.94 (95% CI: 75.97 to 81.31) in 1990 to 59.79 (95% CI: 55.32 to 63.83) in 2019 for kidney cancer, and from 192.27 (95% CI: 137.00 to 241.05) in 1990 to − 103.99 (95% CI: − 183.82 to 51.75) in 2019 for prostate cancer. Moreover, the concentration index changed from 12.44 (95% CI, 11.86 to 12.74) in 1990 to 15.72 (95% CI, 15.14 to 16.01) in 2019 for bladder cancer, from 33.88 (95% CI: 33.35 to 34.17) in 1990 to 31.13 (95% CI: 30.36 to 31.43) in 2019 for kidney cancer, and from 14.61 (95% CI: 13.89 to 14.84) in 1990 to 5.89 (95% CI: 5.16 to 6.26) in 2019 for prostate cancer. Notably, the males presented higher inequality than females in both bladder and kidney cancer from 1990 to 2019. Conclusions Different patterns of inequality were observed in the three cancers, necessitating tailored national cancer control strategies to mitigate disparities. Priority interventions for bladder and kidney cancer should target higher socioeconomic regions, whereas interventions for prostate cancer should prioritize the lowest socioeconomic regions. Additionally, addressing higher inequality in males requires more intensive interventions among males from higher socioeconomic regions.

Published
2024
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28. Applying 5PKC-Based Skeleton Partition Strategy into Spatio-Temporal Graph Convolution Networks for Fitness Action Recognition

Author

Chang, Jia-Wei, Liu, Hao-Ran, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Hirche, Sandra, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Zhang, Junjie James, Series Editor, Tan, Kay Chen, Series Editor, Hung, Jason C., editor, Chang, Jia-Wei, editor, and Pei, Yan, editor

Published
2023
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34. Prevalence and risk factors of tuberculosis among people living with HIV/AIDS in China: a systematic review and meta-analysis

Author

Cong-Cong Qi, Li-Ran Xu, Chang-Jia Zhao, Hai-Yan Zhang, Qing-Ya Li, Mei-Jun Liu, Ye-Xuan Zhang, Zhou Tang, and Xiu-Xia Ma

Subjects
HIV/AIDS, Tuberculosis, Prevalence, Risk factors, Meta-analysis, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Objective To estimate the prevalence and risk factors associated with tuberculosis (TB) among people living with human immunodeficiency virus (HIV) infection/acquired immunodeficiency syndrome (AIDS) in China. Methods A systematic review and meta-analysis were conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. After the literature was screened based on the inclusion and exclusion criteria, STATA® version 17.0 software was used for the meta-analysis. The heterogeneity among study data was assessed using I 2 statistics. Subgroup analysis and meta-regressions were performed to further explore the source of heterogeneity. Results A total of 5241 studies were retrieved. Of these, 44 studies were found to be eligible. The pooled prevalence of HIV/TB co-infection was 6.0%. The risk factors for HIV/TB co-infection included a low CD4+ T cell count, smoking, intravenous drug use and several other sociodemographic and clinical factors. Bacillus Calmette–Guérin (BCG) vaccination history was a protective factor. Conclusion A high prevalence of TB was observed among people living with HIV/AIDS in China. Low CD4+ T cell count, smoking, and intravenous drug use were the primary risk factors for HIV/TB co-infection, whereas BCG vaccination history was a protective factor. Checking for TB should be prioritized in HIV screening and healthcare access. Systematic review registration Registered on PROSPERO, Identifier: CRD42022297754.

Published
2023
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41. Learning Facial Representations from the Cycle-consistency of Face

Author

Chang, Jia-Ren, Chen, Yong-Sheng, and Chiu, Wei-Chen

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Faces manifest large variations in many aspects, such as identity, expression, pose, and face styling. Therefore, it is a great challenge to disentangle and extract these characteristics from facial images, especially in an unsupervised manner. In this work, we introduce cycle-consistency in facial characteristics as free supervisory signal to learn facial representations from unlabeled facial images. The learning is realized by superimposing the facial motion cycle-consistency and identity cycle-consistency constraints. The main idea of the facial motion cycle-consistency is that, given a face with expression, we can perform de-expression to a neutral face via the removal of facial motion and further perform re-expression to reconstruct back to the original face. The main idea of the identity cycle-consistency is to exploit both de-identity into mean face by depriving the given neutral face of its identity via feature re-normalization and re-identity into neutral face by adding the personal attributes to the mean face. At training time, our model learns to disentangle two distinct facial representations to be useful for performing cycle-consistent face reconstruction. At test time, we use the linear protocol scheme for evaluating facial representations on various tasks, including facial expression recognition and head pose regression. We also can directly apply the learnt facial representations to person recognition, frontalization and image-to-image translation. Our experiments show that the results of our approach is competitive with those of existing methods, demonstrating the rich and unique information embedded in the disentangled representations. Code is available at https://github.com/JiaRenChang/FaceCycle ., Comment: ICCV 2021

Published
2021

50. Experimental Investigation of Effectiveness of FRP Composite Repair System on Offshore Pipelines Subjected to Pitting Corrosion Under Axial Compressive Load

Author

Wei, Chang Jia, Liang, Ong Zhen, Jarghouyeh, Ehsan Nikbakht, di Prisco, Marco, Series Editor, Chen, Sheng-Hong, Series Editor, Vayas, Ioannis, Series Editor, Kumar Shukla, Sanjay, Series Editor, Sharma, Anuj, Series Editor, Kumar, Nagesh, Series Editor, Wang, Chien Ming, Series Editor, Wang, Shuren, editor, Li, Jingan, editor, Hu, Kui, editor, and Bao, Xingxian, editor

Published
2023
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